Re: Re: Bad global bond count! (48842 vs 48843)

From: Brian Radak (
Date: Tue Apr 10 2018 - 12:50:45 CDT

Can you describe the procedure for adding extrabonds with VMD? This is not
a feature I'm familiar with.

The indices for extrabonds are indeed "off by one" compared to the PDB
because NAMD internally starts 0 rather than 1 during indexing (and ignores
PDB numbering entirely).

I don't think VMD will show extrabonds either, since these are not in the
PSF and the program thus has no knowledge of them.

On Tue, Apr 10, 2018 at 12:41 PM, Ashutosh Shandilya <>

> Extrabond file for nucleic acid is generated using VMD. I could see the
> numbering index in extrabond is somewhat different than nucleic acid
> numbering. I generated nucleic acid with the same selection using VMD it
> generates only nucleic acid. Could not attache psf file associated to pdb
> file as it exceeds the size limit for namd user mailing list. If any one
> could provide any insight that would help.
> Many thanks,
> Ash
> On Tue, Apr 10, 2018 at 10:47 AM, Ashutosh Shandilya <
> > wrote:
>> Dear NAMD Users
>> I am trying to run targeted MD with extra bond restraints. I am getting
>> this error, I checked for possible solutions online to check for duplicate
>> atoms but could not find any. Even during visualization there are no
>> unusual bonds. I ran step wise minimization and equilibration with
>> restraints and constraints which ran fine. Also tried increasing cut off
>> with no effect.
>> Attached are my extra bond file (only nucleic acid) and pdb and input
>> file. Kindly suggest.
>> Many thanks,
>> Ash

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